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paleoDiv (version 0.4.6)

Extracting and Visualizing Paleobiodiversity

Description

Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database , extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.

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Install

install.packages('paleoDiv')

Monthly Downloads

234

Version

0.4.6

License

GPL (>= 3)

Maintainer

Darius Nau

Last Published

March 23rd, 2025

Functions in paleoDiv (0.4.6)

Download data from the paleobiology database.

A wrapper around pdb(), occ.cleanup() and mk.sptab() to automatically download and clean occurrence data from the paleobiology database and build species-level taxon-range tables for multiple taxa in one step.

Generate a taxon-range table based on an occurrence dataset.

Replicate the standard color scheme from ggplot2

Wrapper around jitterp that plots multiple jitter plots on the same plotting device (analogous to violins())

diversity_table

diversity_table

Extract subsets of an occurrence data.frame.

Combine selected entries in a taxon-range table to remove duplicates

tree.age.combine

Combine two calibration matrixes and fill in NA values in one with values from another

Add a horizontal, period-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.

Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.

Calculate a rolling mean based on distance within a second variable.

Convert geological ages for accurate plotting alongside a calibrated phylogeny

Clean up occurrence dataset by removing commonly used character combinations in the identified name that will result in different factor levels for the same taxon.

Redraw the lines of a phylogenetic tree.

Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.

Plots a phylogenetic tree with spindle-diagrams, optimized for showing taxonomic diversity.

Add a horizontal, stage-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.

Generate a violin plot

Calculate a rolling mean for a vector x.

Wrapper around viol() to conveniently plot multiple violins on a single plot, analogous to the behavior of boxplot()

tree_archosauria

tree_archosauria

Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2

Convert geological ages in taxon-range tables as constructed by mk.sptab() for plotting alongside a time-calibrated phylogeny.

Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2

Count number of entries in occurrence or collection data.frame for specific points in geological time

Calculate total species diversity for any point in time based on a taxon-range table

ages_archosauria

ages_archosauria

Add transparency to any color

Darken or lighten colors by adding/subtracting to or hsv channel values

Count number of taxon records overlapping a specific time interval.

Subtract one occurrence data.frame from another, for disentangling overlapping taxonomies or quantifying stem-lineage diversity.

plot data as a jitter-plot

Form the union of two occurrence data.frames or remove duplicates from occurrence data.frame. Useful if parts of a clade are not included in the downloaded dataset and need to be added separately.